Shaving the block is called "decking" or "block decking". Its where the piston height is raised to decease the swept volume of the cylinder, the compression ratio is also increased cause of the lowered deck height.
Yes and no, the crank pin (or what the conrod spins on) can be machined undersized but moving the base circle outwards as its decreased in size. Another way is of building up weld to the outside of the crank pin and then having it machined down to the correct size but the base circle is moved outwards.
The downsides
If you machine the crank pin too much can weaken it
Have to be careful of the gap between the block skirt and the conrods
Piston speeds can get to be a problem at the end the strokes, more so with short conrods. Which is why longer conrods are included in a stroker kit.
All in all stroking the 3k crank would be a pointless waste of money when the 4k crank is available and you'll have a better start using the 4k block or the 5k block.
Phil - didn't mean to sound negative or that. I say go for it, if you have ready access to tooling, parts etc go for it.